Research workbench
Crystal structure of the CDK2/CYCLIN a complex with oxindole inhibitor
Analyse Crystal structure of the CDK2/CYCLIN a complex with oxindole inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FX3
- Type
- protein
- Length
- 1,111 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent kinase 2; Cyclin-A2
- EC
- 2.7.11.22
- UniProt
- P24941, P20248
- Ligands
- 60K
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 298 | 34% helix, 16% strand | P24941 |
| B | Cyclin-A2 | protein | 257 | 67% helix, 0% strand | P20248 |
| D | Cyclin-A2 | protein | 258 | 65% helix, 0% strand | P20248 |
Ligands and binding sites
- 60K · (3Z)-2-oxo-3-[2-(4-sulfamoylphenyl)hydrazinylidene]-2,3-dihydro-1H-indole-5-carboxylic acid · ligand · 2 copies · chains A, C
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.81 | 0.98 | 23 | empty |
| 2 | 130 | 0.80 | 0.98 | 24 | empty |
| 3 | 571 | 0.71 | 0.79 | 54 | DTT |
| 4 | 241 | 0.67 | 0.84 | 29 | 60K |
| 5 | 252 | 0.67 | 0.83 | 34 | 60K |
Interfaces
5 interfaces between chains.
- C–D · 1654 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1560 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 488 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 478 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 106 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4FX3 · Crystal Structure of the CDK2/Cyclin A complex with oxindole inhibitor · the same entry in another collection · chain D against D, TM-score 1.00
- P20248 · AlphaFold monomer V2.0 prediction for cyclin-A2 (P20248) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P24941 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 2 (P24941) · a predicted model of the same protein · chain A against A, TM-score 0.92
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P24941
- Every structure of UniProt P20248
- Elsewhere: RCSB PDB 4FX3 · PDBe 4FX3 · UniProt P24941 · UniProt P20248
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